Journal ArticleDOI
Improved Docking of Polypeptides with Glide
TLDR
The optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.Abstract:
Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein–protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM-GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 A for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a su...read more
Citations
More filters
Journal ArticleDOI
COVID-19 in people with diabetes: understanding the reasons for worse outcomes.
Matteo Apicella,Maria Cristina Campopiano,Michele Mantuano,Laura Mazoni,Alberto Coppelli,Stefano Del Prato +5 more
TL;DR: The reason for worse prognosis in people with diabetes is likely to be multifactorial, thus reflecting the syndromic nature of diabetes, and age, sex, ethnicity, comorbidities such as hypertension and cardiovascular disease, obesity, and a pro-inflammatory and pro-coagulative state all probably contribute to the risk of worse outcomes.
Journal ArticleDOI
Macromolecular modeling and design in Rosetta: recent methods and frameworks
Julia Koehler Leman,Brian D. Weitzner,Brian D. Weitzner,Steven M. Lewis,Steven M. Lewis,Jared Adolf-Bryfogle,Nawsad Alam,Rebecca F. Alford,Melanie L. Aprahamian,David Baker,Kyle A. Barlow,Patrick Barth,Patrick Barth,Benjamin Basanta,Brian J. Bender,Kristin Blacklock,Jaume Bonet,Jaume Bonet,Scott E. Boyken,Phil Bradley,Christopher Bystroff,Patrick Conway,Seth Cooper,Bruno E. Correia,Bruno E. Correia,Brian Coventry,Rhiju Das,René M. de Jong,Frank DiMaio,Lorna Dsilva,Roland L. Dunbrack,Alex Ford,Brandon Frenz,Darwin Y. Fu,Caleb Geniesse,Lukasz Goldschmidt,Ragul Gowthaman,Jeffrey J. Gray,Dominik Gront,Sharon L. Guffy,Scott Horowitz,Po-Ssu Huang,Thomas Huber,Timothy M. Jacobs,Jeliazko R. Jeliazkov,David K. Johnson,Kalli Kappel,John Karanicolas,Hamed Khakzad,Hamed Khakzad,Karen R. Khar,Sagar D. Khare,Firas Khatib,Alisa Khramushin,Indigo Chris King,Robert Kleffner,Brian Koepnick,Tanja Kortemme,Georg Kuenze,Brian Kuhlman,Daisuke Kuroda,Jason W. Labonte,Jason W. Labonte,Jason K. Lai,Gideon Lapidoth,Andrew Leaver-Fay,Steffen Lindert,Thomas W. Linsky,Nir London,Joseph H. Lubin,Sergey Lyskov,Jack Maguire,Lars Malmström,Lars Malmström,Lars Malmström,Enrique Marcos,Orly Marcu,Nicholas A. Marze,Jens Meiler,Rocco Moretti,Vikram Khipple Mulligan,Santrupti Nerli,Christoffer Norn,Shane O’Conchúir,Noah Ollikainen,Sergey Ovchinnikov,Michael S. Pacella,Xingjie Pan,Hahnbeom Park,Ryan E. Pavlovicz,Manasi A. Pethe,Brian G. Pierce,Kala Bharath Pilla,Barak Raveh,P. Douglas Renfrew,Shourya S. Roy Burman,Aliza B. Rubenstein,Marion F. Sauer,Andreas Scheck,Andreas Scheck,William R. Schief,Ora Schueler-Furman,Yuval Sedan,Alexander M. Sevy,Nikolaos G. Sgourakis,Lei Shi,Justin B. Siegel,Daniel-Adriano Silva,Shannon Smith,Yifan Song,Amelie Stein,Maria Szegedy,Frank D. Teets,Summer B. Thyme,Ray Yu-Ruei Wang,Andrew M. Watkins,Lior Zimmerman,Richard Bonneau +117 more
TL;DR: This Perspective reviews tools developed over the past five years in the Rosetta software, including over 80 methods, and discusses improvements to the score function, user interfaces and usability.
Journal ArticleDOI
Conducting polymers: a comprehensive review on recent advances in synthesis, properties and applications
K Namsheer,Chandra Sekhar Rout +1 more
TL;DR: In this article, a review of composites of conducting polymers with carbonaceous materials, metal oxides, transition metals and transition metal dichalcogenides is presented, which help to explain the conduction mechanism, relevant synthesis approaches, and physical properties including electrical, optical and mechanical properties.
Journal ArticleDOI
Properties of recycled concrete aggregate and their influence in new concrete production
TL;DR: In this paper, the authors present a review of the potential and challenge of using recycled concrete aggregate (RCA) as the substitute for natural aggregate (NA) in concrete mixtures.
Journal ArticleDOI
Binder jet 3D printing—Process parameters, materials, properties, modeling, and challenges
Amir Mostafaei,Amy M. Elliott,John E. Barnes,Fangzhou Li,Wenda Tan,Corson L. Cramer,Peeyush Nandwana,Markus Chmielus +7 more
TL;DR: In this paper, a detailed review of the physical processes during 3D printing and the fundamental science of densification after sintering and post-heat treatment steps are provided to understand the microstructural evolution and properties of binder jetted parts.
References
More filters
Journal ArticleDOI
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
TL;DR: In this article, the parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described, and the parameters for both torsional and non-bonded energy properties have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER force field.
Journal ArticleDOI
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
Richard A. Friesner,Jay L. Banks,Robert B. Murphy,Thomas A. Halgren,Jasna Klicic,Daniel T. Mainz,Matthew P. Repasky,Eric H. Knoll,Mee Shelley,Jason K. Perry,David E. Shaw,Perry Francis,Peter S Shenkin +12 more
TL;DR: Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand to find the best docked pose using a model energy function that combines empirical and force-field-based terms.
Journal ArticleDOI
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.
Thomas A. Halgren,Robert B. Murphy,Richard A. Friesner,Hege S. Beard,Leah L. Frye,W. Thomas Pollard,Jay L. Banks +6 more
TL;DR: Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01.
Journal ArticleDOI
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.
TL;DR: A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment and they have been parametrized directly to reproduce experimental thermodynamic and structural data on fluids.
Journal ArticleDOI
Announcing the worldwide Protein Data Bank.
TL;DR: The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform, and provides a mechanism to ensure consistent data for software developers and users worldwide.
Related Papers (5)
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more